GAPO Syndrome via the ANTXR1 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 9865 | ANTXR1 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).
Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).
The Sanger Sequencing method for this test is NY State approved.
For Sanger Sequencing click here.Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
GAPO syndrome is an acronym for a rare, but distinct autosomal-recessive condition, which is clinically characterized by Growth Retardation, Alopecia (early baldness), Pseudo-Anodontia (failure of tooth eruption), and progressive Optic Atrophy (Tipton and Gorlin 1984). In the majority of the cases diagnosis is possible as early as infancy due to retarded bone age and characteristic facial appearance (high and bossed forehead, midface hypoplasia). Optic atrophy is not always present (Ilker et al. 1999).
Genetics
Pathogenic variants in ANTXR1 (anthrax toxin receptor 1) have been reported to be causative for autosomal-recessive GAPO syndrome. The ANTXR1 gene (also known as TEM8 - Tumor endothelial marker 8), encodes a type I transmembrane protein, which is a highly conserved cell-surface protein. ANTXR1 is predominantly expressed on tumor vasculature (Chaudhary et al. 2012). This protein functions as an adhesion molecule mediating cell spreading by coupling extracellular ligands to the actin cytoskeleton. Extracellular-matrix-homeostasis defect is a characteristic feature of GAPO syndrome, which is possibly due to the ANTXR1 pathogenic variants that lead to altered cell-adhesion properties that in turn result in progressive extracellular-matrix buildup (Werner et al. 2006). So far, about 5 mutations (Missense/nonsense, splicing and small insertions) have been reported in ANTXR1 that are causative for GAPO syndrome (Human Gene Mutation Database; Stránecký et al. 2013; Bayram et al. 2014).
Clinical Sensitivity - Sequencing with CNV PGxome
Clinical sensitivity cannot be precisely estimated in GAPO syndrome patients as it is a rare disorder with a limited number of documented cases. Analytical sensitivity should be high because all ANTXR1 mutations reported are detectable by sequencing. No gross deletions or duplications have been reported so far (Human Gene Mutation Database).
Testing Strategy
This test provides full coverage of all coding exons of the ANTXR1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).
Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).
Indications for Test
All patients with symptoms suggestive of GAPO syndrome are candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in ANTXR1.
All patients with symptoms suggestive of GAPO syndrome are candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in ANTXR1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| ANTXR1 | 606410 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| GAPO Syndrome | AR | 230740 |
Citations
- Bayram Y, Pehlivan D, Karaca E, Gambin T, Jhangiani SN, Erdin S, Gonzaga-Jauregui C, Wiszniewski W, Muzny D, Baylor-Hopkins Center for Mendelian Genomics, Elcioglu NH, Yildirim MS, Bozkurt B, Zamani AG, Boerwinkle E, Gibbs RA, Lupski JR. 2014. Whole exome sequencing identifies three novel mutations in ANTXR1 in families with GAPO syndrome. American Journal of Medical Genetics Part A 164: 2328–2334. PubMed ID: 25045128
- Chaudhary A, Hilton MB, Seaman S, Haines DC, Stevenson S, Lemotte PK, Tschantz WR, Zhang XM, Saha S, Fleming T, St. Croix B. 2012. TEM8/ANTXR1 Blockade Inhibits Pathological Angiogenesis and Potentiates Tumoricidal Responses against Multiple Cancer Types. Cancer Cell 21: 212–226. PubMed ID: 22340594
- Human Gene Mutation Database (Bio-base).
- Ilker SS, Oztürk F, Kurt E, Temel M, Gül D, Sayli BS. 1999. Ophthalmic findings in GAPO syndrome. Jpn. J. Ophthalmol. 43: 48–52. PubMed ID: 10197743
- Stránecký V, Hoischen A, Hartmannová H, Zaki MS, Chaudhary A, Zudaire E, Nosková L, Barešová V, Pristoupilová A, Hodanová K, Sovová J, Hulková H, Piherová L, Hehir-Kwa JY, de Silva D, Senanayake MP, Farrag S, Zeman J, Martásek P, Baxová A, Afifi HH, St Croix B, Brunner HG, Temtamy S, Kmoch S. 2013. Mutations in ANTXR1 Cause GAPO Syndrome. The American Journal of Human Genetics 92: 792–799. PubMed ID: 23602711
- Tipton RE, Gorlin RJ. 1984. Growth retardation, alopecia, pseudo-anodontia, and optic atrophy--the GAPO syndrome: report of a patient and review of the literature. Am. J. Med. Genet. 19: 209–216. PubMed ID: 6507471
- Werner E, Kowalczyk AP, Faundez V. 2006. Anthrax Toxin Receptor 1/Tumor Endothelium Marker 8 Mediates Cell Spreading by Coupling Extracellular Ligands to the Actin Cytoskeleton. Journal of Biological Chemistry 281: 23227–23236. PubMed ID: 16762926
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
Requisition Form
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
For Requisition Forms, visit our Forms page
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
PGxome (Exome) Sequencing Panel
PGnome (Genome) Sequencing Panel
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ORDER OPTIONS
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
No Additional Test Options are available for this test.